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Crystal endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L343F from Prunus communis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.25 291 100mM tris-bicine pH 8.5, 60mM CaCl2, 60mM MgCl2, 18% v/v PEG 500MME, 9% w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.51 51.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.688 α = 90 b = 91.223 β = 90 c = 131.414 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2019-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9789 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 50 95.6 0.894 24 12 77470
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 0.89
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6J8K 1.6 46.52 72207 3880 95.86 0.149 0.1476 0.1622 0.1749 0.1897 RANDOM 14.897
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.15 -0.21 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.477 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_3_deg 11.257 r_dihedral_angle_1_deg 7.406 r_angle_refined_deg 1.917 r_angle_other_deg 1.536 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.477 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_3_deg 11.257 r_dihedral_angle_1_deg 7.406 r_angle_refined_deg 1.917 r_angle_other_deg 1.536 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3974 Nucleic Acid Atoms Solvent Atoms 725 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-3000 data reduction